Alanine
Ala, A, Non-polar
Valine
Val, V, Non-polar
Phenylalanine
Phe, F, Non-polar
Tryptophan
Trp, W, Non-polar
Leucine
Leu, L, Non-polar
Isoleucine
Ile, I, Non-polar
Methionine
Met, M, Non-polar
Proline
Pro, P, Non-polar
Serine
Ser, S, Polar
Threonine
Thr, T, Polar
Tyrosine
Tyr, Y, Polar
Asparagine
Asn, N, Polar
Glutamine
Gln, Q, Polar
Cysteine
Cys, C, Polar (creates disulfide bonds with other cysteines
Histidine
His, H, Polar (can be charged)
Lysine
Lys, K, Basic (pos charge)
Arginine
Arg, R, Basic (pos charge)
Aspartate (aspartic acid)
Asp, D, Acidic (neg charge)
Glutamate (glutamic acid)
Glu, E, Acidic (neg charge)
Glycine
Gly, G, Not charged
Rank the following according to their strength as acids--rank from strongest (1) to weakest (5).
A - 4 B - 3 C - 5 D - 2 E - 1
Which of the following would NOT form a suitable buffer?
Hydrochloric acid/chloride
Under what conditions would a carboxyl group (COOH, pK 3.5) be mostly protonated?
pH < pK
Under what conditions would a carboxyl group (COOH, pK 3.5) be mostly deprotonated?
pH > pK
In aqueous solution, globules of up to several thousand amphiphilic molecules arranged with the hydrophilic groups on the surface and the hydrophobic groups buried in the center are called _____.
micelles
What term is used to describe the exclusion of nonpolar substances from an aqueous solution?
hydrophobic effect
Which of the following is an example of the hydrophobic effect?
all are examples of the hydrophobic effect
A molecule that has both a polar and nonpolar region is called _____________.
amphiphilic
If the pK value for acetic acid (CH3COOH) is 4.76 at what pH would one observe equal amounts of CH3COO- and CH3COOH?
4.76
During metabolic acidosis, ______ ventilation excretes acid in the form of _____ .
increased; CO2
The LOWER the pK value of an acid the STRONGER the acid.
True
Which of the following bond forces are important in tertiary structure:
Hydrophobic effect Hydrogen bonds Disulfide bonds
Which of the following amino acid substitutions would be most likely to effect protein function?
B
Select all the commonalities between alpha helices and b-pleated sheets. (i.e. select what is similar in both types of secondary structure)
prolines and glycines aren't suitable for the secondary structure hydrogen bonds between main chain CO and NH groups peptide bond is planar
The formation of a dipeptide from two amino acids involves
A) side-chain complementarity.
B) loss of water.
C) oxidation of the alpha-carbon.
D) reduction of the alpha-carbon.
E) base catalysis.
B
The protein shown above is the human coronavirus protease. The structure contains 2 subunits, that have identical sequences. This protein can be classified as:
quaternary:homodimer
At what pH would an amino acid bear both a COOH and an NH2 group?
Never
All secondary structures in proteins involve helical forms.
False
Cys-Ala-Gly-Arg-Gln-Met
In the above peptide, the amino-terminal amino acid is ____ and the carboxyl-terminal amino acid is ____
Cys; Met
For the amino acid structures shown above, the protonation state of structure A is shown at ______ pH, and the protonation state of structure B is shown at _______ pH.
low; high
Choose the amino acid that would be more likely to appear on the solvent-exposed (water facing) surface of a protein.
Leu or Lys Ser or Ala Phe or Tyr Trp or Gln Asn or Ile
Lys
Ser
Tyr
Gln
Asn
Primary
The order in which the amino acids in a protein are linked by peptide bonds
Secondary
The arrangement of the backbone atoms in a polypeptide chain
Tertiary
The arrangement of all the atoms in a protein (interactions between the R groups, hydrophobic ones inside of the protein)
Quaternary
the interaction of several polypeptide chains in a multisubunit protein
Examine the four amino acids given below:
Indicate which of these amino acids are associated with the following properties:
branched aliphatic sidechain - C basic sidechain - D aromatic R group - B cyclic (nonaromatic) R group - A
Which of the following amino acids carry a net positive charge at pH 7.0?
Arg, Lys
What is the net charge on the following peptide at pH 9.5?
Lys-Ala-Glu-Gln-Cys-Ile
-2
What is the net charge of the pentapeptide Ala-Cys-Ser-Glu-Asn at pH 7?
-1
Any peptide which contains 2 sulfur-containing amino acids can form an internal disulfide bond.
False
The interactions that stabilize multisubunit complexes are different than those that stabilize tertiary structure.
False
Myoglobin is _____; hemoglobin is _____.
monomeric; tetrameric
The individual hemoglobin subunits and myoglobin share similar primary structure but have rather different secondary structure.
False
Which of the following fibers is correctly paired with the protein that forms the fiber?
extracellular support fibers: collagen microtubules: tubulin microfilaments: actin intermediate filaments: keratin (all are true)
Which amino acid is critical for crosslinking of keratin fibers?
Cys (disulfide bonds)
The idea that binding of one molecule of oxygen to hemoglobin enhances further binding of oxygen to hemoglobin is called _____.
cooperativity
What is the most prevalent secondary structure observed in the proteins of intermediate filaments?
alpha helices
Which of the following statements about actin are true?
Monomeric G-actin polymerizes to form F-actin. Actin filaments are polar (the ends can be distinguished).
Several oxygen dissociation curves are shown in the figure below. Assuming that curve 3 corresponds to isolated hemoglobin placed in a solution containing physiologic concentrations of CO2 and BPG at a pH of 7.0, indicate which of the curves reflects the following changes in conditions:
Increased BPG concentration 4
Increased pH 2
Dissociation of hemoglobin into subunits. 1
Match the feature of hemoglobin with the proper structural level.
Amino acid sequence in each of the alpha and beta polypeptide chains. Primary Structure
8 alpha helices in each of the subunits. Secondary Structure
Spatial relationship between every atom in the individual subunits. Tertiary Structure
Spatial relationship between the four polypeptide chains. Quaternary Structure
The presence of 2,3-BPG causes hemoglobin's affinity for oxygen to______.
decrease
Which amino acid is involved in heme coordination in both hemoglobin and myoglobin and is highly conserved?
Histidine
Calculate the fractional saturation for myoglobin when pO2 is a. 20 torr and b. 80 torr. Assume K=2.8.
a. 0.88 b. 0.97
Both myoglobin and hemoglobin exhibit cooperative binding to oxygen.
False
Conservative amino acid mutations (i.e. Val to Leu) are likely to affect stability or function of a protein.
False
Which of the following fatty acids have the lowest melting point?
Linoleate (18:2)
Which of the following types of lipids can be found in cell membranes?
glycerophospholipids cholesterol cerebrosides gangliosides
Select the statements the describe fatty acids:
can either be saturated or unsaturated. mostly found with an even number of carbons
In what way(s) do sphingolipids differ from glycerophospholipids?
Sphingolipids are not built on a glycerol backbone. Sphingolipids contain an acyl group attached via an amide bond on the serine potion of the sphingosine.
Show which are characteristics of peripheral membrane proteins and which are characteristics of integral membrane proteins.
peripheral bind to the surface of membranes
integral have transmembrane domains
Which of the following is most likely to be an unnatural fatty acid?
17:3△t9,12,15 (uneven number of carbons)
Sphingosine is not a component of:
glycerophospholipids
Select the fatty acid in each pair that has the higher melting temperature.
16:1c9 or 16:2c9,12
16:1c9
18:0 or 18:1c9
18:0
18:0 or 20:0
20:0
Membranes are generally symmetrical, i.e., the outer face is composed of the same number and types of phospholipids as the inner face.
False
Phospholipids can freely diffuse from the interior leaflet of the plasma membrane to the exterior leaflet without the assistance of enzymes.
False
Triglycerides are fat storage molecules not typically found in membranes.
True
Match the description given with the correct lipid. (Answers may be used more than once)
Primary storage form of lipids. Triacylglycerols.
Provides stability in the plasma membrane. Cholesterol
Isoprene derivative Cholesterol
Commonly found in nervous tissue Sphingomyelin
Sphingosine backbone with several carbohydrates attached Ganglioside
Glycerol backbone with two fatty acyl groups Glycerophospholipid
A membrane's fluidity is largely determined by the percentage of _____________.
unsaturated fats
The concentration of Ca2+ in the endoplasmic reticulum (outside) is 1 mM, and the concentration of Ca2+ in the cytosol (inside) is 0.1 μM. Calculate ΔG at 37°C when the membrane potential is −50 mV (cytosol negative)
-33,388.1
Which of the following is/are true regarding the glucose transporter?
it transports glucose down it's concentration gradient binding of glucose causes a conformational change so that the transporter is never open on both sides of the membrane
Match the transporter (A- blue, B- green, C- light purple) with it's description.
A - Symporter
B - Uniporter
C - Antiporter
Indicate whether the following compounds are likely to cross a membrane by simple diffusion or facilitated diffusion transport:
aspartic acid facilitated
carbon dioxide simple
glucose facilitated
Which of the following will cause the opening or closing of a gated ion channel?
voltage change
What substance will be transported through an aquaporin?
water
In the sodium-potassium pump:
sodium is transported out of the cell and potassium into the cell, both against concentration gradients
Active transport is uniquely characterized by:
the tight coupling of an input of energy, with the species going from a lesser concentration to a greater concentration.
Facilitated (Mediated) diffusion across a biological membrane:
is driven by a difference in solute concentration.
Energy requiring transport mechanisms include
Active transport
Inside a nerve cell at rest, [Na +] is ____ and [K+] _____ relative to the concentrations seen outside the cell.
low, high
The Hydrophobic Effect
The exclusion of nonpolar substances from an aqueous solution
Amphiphilic
experience both hydrophilic interactions and the hydrophobic effect. most lipids are amphiphilic.
the pH scale
The ionization of water can be described by a dissociation constant, K:
(products)/(reactants)
acid
substance that can donate a proton
base
a substance that can accept a proton
pK helps to
determine the strength of an acid (lower pK = stronger acid, higher pK = weaker acid)
Henderson-Hasselbalch Equation
*pK is the specific pH where there are equal concentrations of base and acid *log > 1 --> always positive, pH rises *log < 1 --> always negative, pH lowers
pH < pK
everything will be protonated
buffer
weak acid/conj base system aids in resisting changes in the pH of a system
Amino Acids (L and D groups)
L --> amino group to the left of the alpha carbon D --> amino group to the right of the alpha carbon
L is the most common in nature